Exome Evaluation of Autism-Associated Genes in Amazon American Populations
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study and Reference Populations
2.2. Extraction of the DNA and Preparation of the Exome Library
2.3. Bioinformatics Analysis
2.4. Statistical Analysis
2.5. Selection of Genes and Variants
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | SNP ID | Region | Alleles | Impact Predicted by SNPeff | IND | AFR | AMR | EAS | EUR | SAS |
---|---|---|---|---|---|---|---|---|---|---|
CHD8 | rs35057134 | Intronic | GA > G | Modifier | 0.0143 | 0.2250 | 0.2070 | 0.3480 | 0.2740 | 0.2550 |
CHD8 | rs80311097 | Intronic | C > A | Modifier | 0.0000 | 0.0610 | 0.0010 | 0.0000 | 0.0010 | 0.0000 |
CHD8 | rs10467770 | CDS | C > T | Moderate | 0.0781 | 0.2240 | 0.1900 | 0.3450 | 0.2450 | 0.2490 |
CHD8 | rs111250264 | CDS | G > A | Moderate | 0.0086 | 0.0050 | 0.0000 | 0.0000 | 0.0000 | 0.0000 |
CHD8 | rs57764234 | Intronic | C > T | Modifier | 0.0246 | 0.3160 | 0.0290 | 0.0000 | 0.0210 | 0.0050 |
CHD8 | rs111776414 | Intronic | G > GA | Modifier | 0.0417 | 0.1610 | 0.0120 | 0.0010 | 0.0020 | 0.0110 |
CHD8 | rs1998332 | Intronic | G > A | Modifier | 0.6172 | 0.5730 | 0.7780 | 0.8880 | 0.9060 | 0.9170 |
CHD8 | rs149307240 | CDS | C > T | Moderate | 0.0259 | 0.0000 | 0.0160 | 0.0000 | 0.0010 | 0.0000 |
SCN2A | rs17183814 | CDS | G > A | Moderate | 0.2500 | 0.0210 | 0.0820 | 0.1380 | 0.0570 | 0.1420 |
SCN2A | rs75109281 | Intronic | C > T | Modifier | 0.0833 | 0.0120 | 0.0030 | 0.0000 | 0.0000 | 0.0000 |
SCN2A | rs3769951 | Intronic | C > T | Modifier | 0.0135 | 0.1640 | 0.2480 | 0.2610 | 0.2920 | 0.3310 |
SCN2A | rs28472553 | Intronic | A > C | Modifier | 0.0833 | 0.0290 | 0.0030 | 0.0000 | 0.0010 | 0.0000 |
SCN2A | rs139906774 | Intronic | G > GA | Modifier | 0.0000 | 0.0520 | 0.3000 | 0.3420 | 0.2420 | 0.1860 |
SCN2A | rs2304014 | Intronic | T > A | Modifier | 0.0270 | 0.2280 | 0.1330 | 0.1410 | 0.1760 | 0.1390 |
SCN2A | rs6432821 | Intronic | T > C | Modifier | 1.0000 | 0.9520 | 0.9970 | 1.0000 | 1.0000 | 0.9990 |
SCN2A | rs150453735 | Intronic | C > T | Modifier | 0.1852 | 0.0020 | 0.0530 | 0.0000 | 0.0000 | 0.0000 |
SCN2A | rs1867864 | Intronic | C > T | Modifier | 0.4453 | 0.6130 | 0.4600 | 0.3430 | 0.5640 | 0.4870 |
SCN2A | rs1838846 | Intronic | A > G | Modifier | 0.0000 | 0.7930 | 0.7940 | 0.7430 | 0.8300 | 0.6980 |
SCN2A | rs7593568 | Intronic | A > G | Modifier | 0.0000 | 0.7950 | 0.7950 | 0.7430 | 0.8300 | 0.6950 |
FOXP1 | rs1435680522 | 3UTR | GT > G | Modifier | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.0000 |
FOXP1 | rs112773801 | 3UTR | G > GT | Modifier | 0.0167 | 0.4240 | 0.1860 | 0.4510 | 0.1340 | 0.3290 |
FOXP1 | rs58847217 | Intronic | T > C | Modifier | 0.0278 | 0.1010 | 0.0040 | 0.0000 | 0.0000 | 0.0000 |
FOXP1 | rs76145927 | CDS | T > C | Moderate | 0.0000 | 0.0000 | 0.0060 | 0.0390 | 0.0030 | 0.0000 |
FOXP1 | rs72960080 | Intronic | T > C | Modifier | 0.0833 | 0.1190 | 0.0040 | 0.0000 | 0.0000 | 0.0000 |
FOXP1 | rs13068094 | Intronic | C > T | Modifier | 0.0833 | 0.1040 | 0.5400 | 0.0550 | 0.5750 | 0.2820 |
FOXP1 | rs7638391 | Intronic | G > T | Modifier | 1.0000 | 0.9970 | 0.9650 | 1.0000 | 0.9230 | 0.9780 |
FOXP1 | rs56850311 | Intronic | A > T | Modifier | 0.0000 | 0.3960 | 0.2520 | 0.1060 | 0.2890 | 0.2230 |
FOXP1 | rs7639736 | Intronic | C > A | Modifier | 0.0000 | 0.0760 | 0.0560 | 0.0730 | 0.0130 | 0.0200 |
FOXP1 | rs939845 | Intronic | A > G | Modifier | 0.3984 | 0.1630 | 0.2250 | 0.1110 | 0.0640 | 0.0440 |
FOXP1 | rs2037474 | Intronic | A > G | Modifier | 0.5156 | 0.2720 | 0.3430 | 0.4360 | 0.1360 | 0.2450 |
FOXP1 | rs151011253 | Intronic | T > TA | Modifier | 0.0139 | 0.0850 | 0.0560 | 0.0310 | 0.0540 | 0.0960 |
SYNGAP1 | rs76557362 | Intronic | C > T | Modifier | 0.0833 | 0.2530 | 0.0130 | 0.0000 | 0.0000 | 0.0000 |
SYNGAP1 | rs453590 | Intronic | C > T | Modifier | 0.0000 | 0.2700 | 0.4060 | 0.6410 | 0.3860 | 0.5430 |
SYNGAP1 | rs115441992 | Intronic | C > T | Modifier | 0.0833 | 0.0140 | 0.0090 | 0.0000 | 0.0130 | 0.0020 |
SYNGAP1 | rs9394145 | Intronic | C > T | Modifier | 0.5078 | 0.0130 | 0.3240 | 0.2500 | 0.3150 | 0.3220 |
Gene | DbSNP | IND vs. AFR * | IND vs. AMR * | IND vs. EAS * | IND vs. EUR * | IND vs. SAS * |
---|---|---|---|---|---|---|
CHD8 | rs35057134 | 5.98 × 10−6 | 2.74 × 10−5 | 5.31 × 10−10 | 1.39 × 10−7 | 7.66 × 10−7 |
CHD8 | rs80311097 | 0.24887 | 0.28751 | 0.21283 | 0.21318 | 0.21826 |
CHD8 | rs10467770 | 0.00572 | 0.03028 | 2.97 × 10−6 | 0.00220 | 0.00138 |
CHD8 | rs111250264 | 0.30959 | 0.28751 | 0.21283 | 0.21318 | 0.21826 |
CHD8 | rs57764234 | 6.46 × 10−8 | 1.00000 | 0.03481 | 0.64915 | 0.06785 |
CHD8 | rs111776414 | 0.01566 | 0.07929 | 0.00504 | 0.00507 | 0.05415 |
CHD8 | rs1998332 | 0.50781 | 0.01151 | 4.40 × 10−7 | 3.06 × 10−8 | 6.23 × 10−9 |
CHD8 | rs149307240 | 0.02173 | 0.36125 | 0.03481 | 0.03493 | 0.03665 |
SCN2A | rs17183814 | 1.19 × 10−10 | 0.00026 | 0.02585 | 5.70 × 10−6 | 0.04046 |
SCN2A | rs75109281 | 0.00339 | 0.00042 | 8.63 × 10−5 | 8.70 × 10−5 | 9.84 × 10−5 |
SCN2A | rs3769951 | 0.00037 | 1.60 × 10−6 | 4.39 × 10−7 | 3.69 × 10−8 | 2.16 × 10−9 |
SCN2A | rs28472553 | 0.05210 | 0.00042 | 8.63 × 10−5 | 8.70 × 10−5 | 9.84 × 10−5 |
SCN2A | rs139906774 | 0.35386 | 3.54 × 10−8 | 6.13 × 10−10 | 1.54 × 10−6 | 0.00011 |
SCN2A | rs2304014 | 3.85 × 10−5 | 0.01857 | 0.00941 | 0.00166 | 0.01459 |
SCN2A | rs6432821 | 0.10268 | 1.00000 | 1.00000 | 1.00000 | 1.00000 |
SCN2A | rs150453735 | 9.91 × 10−13 | 0.00066 | 1.86 × 10−11 | 1.90 × 10−11 | 2.57 × 10−11 |
SCN2A | rs1867864 | 0.01590 | 1.00000 | 0.09628 | 0.10907 | 0.69027 |
SCN2A | rs1838846 | 8.09 × 10−38 | 3.83 × 10−35 | 5.39 × 10−32 | 1.00 × 10−40 | 2.50 × 10−28 |
SCN2A | rs7593568 | 5.55 × 10−38 | 3.83 × 10−35 | 5.39 × 10−32 | 1.00 × 10−40 | 3.54 × 10−28 |
FOXP1 | rs1435680522 | 0.16887 | 0.28751 | 0.21283 | 0.21318 | 0.21826 |
FOXP1 | rs112773801 | 2.15 × 10−13 | 0.00013 | 3.53 × 10−14 | 0.00344 | 2.18 × 10−9 |
FOXP1 | rs58847217 | 0.07415 | 0.06453 | 0.03481 | 0.03493 | 0.03665 |
FOXP1 | rs76145927 | 0.16887 | 0.39900 | 0.49517 | 0.30231 | 0.21827 |
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da Costa, G.E.; Fernandes, G.L.; Rodrigues, J.C.G.; da V. B. Leal, D.F.; Pastana, L.F.; Pereira, E.E.B.; Assumpção, P.P.; Burbano, R.M.R.; dos Santos, S.E.B.; Guerreiro, J.F.; et al. Exome Evaluation of Autism-Associated Genes in Amazon American Populations. Genes 2022, 13, 368. https://doi.org/10.3390/genes13020368
da Costa GE, Fernandes GL, Rodrigues JCG, da V. B. Leal DF, Pastana LF, Pereira EEB, Assumpção PP, Burbano RMR, dos Santos SEB, Guerreiro JF, et al. Exome Evaluation of Autism-Associated Genes in Amazon American Populations. Genes. 2022; 13(2):368. https://doi.org/10.3390/genes13020368
Chicago/Turabian Styleda Costa, Giovana E., Giordane L. Fernandes, Juliana C. G. Rodrigues, Diana F. da V. B. Leal, Lucas F. Pastana, Esdras E. B. Pereira, Paulo P. Assumpção, Rommel M. R. Burbano, Sidney E. B. dos Santos, João F. Guerreiro, and et al. 2022. "Exome Evaluation of Autism-Associated Genes in Amazon American Populations" Genes 13, no. 2: 368. https://doi.org/10.3390/genes13020368
APA Styleda Costa, G. E., Fernandes, G. L., Rodrigues, J. C. G., da V. B. Leal, D. F., Pastana, L. F., Pereira, E. E. B., Assumpção, P. P., Burbano, R. M. R., dos Santos, S. E. B., Guerreiro, J. F., Fernandes, M. R., & dos Santos, N. P. C. (2022). Exome Evaluation of Autism-Associated Genes in Amazon American Populations. Genes, 13(2), 368. https://doi.org/10.3390/genes13020368